"I advise you to come back home, adopt the Islamic and Pashtun culture, join any female Islamic madrassa near your home town, study and learn the book of Allah…" reads the letter, which was recently released to a number of media outlets.
The letter is attributed to Adnan Rasheed, a former officer with the Pakistani air force who was convicted in connection with a 2003 plot to assassinate then-Pakistani President Pervez Musharraf. Rasheed was freed from prison last year by the Taliban, along with several hundred other inmates.
Rasheed is believed to be a member of the Tehrik-e-Taliban Pakistan, the group that claimed responsibility for the October 2012 attack on Malala, in which a gunman shot the 15-year-old in the head as she rode on a school bus near her home in Pakistan's Swat Valley.
Malala survived after being airlifted to the Pakistani capital for treatment, and eventually to a hospital in Birmingham, England, where she now lives.
Malala addresses UN
Following the attack, Malala gained international attention for her work as a child activist advocating for girls' rights to education, culminating in a speech last Friday, her 16th birthday, before the United Nations General Assembly in New York City.
"They thought that the bullets would silence us, but they failed, and out of that silence came thousands of voices," she said.
"I'm not against anyone. Neither am I here to speak in terms of personal revenge against the Taliban or any other terrorist group. I'm here to speak for the right of education for every child."
In Rasheed's letter, which is dated July 15, he repeatedly alludes to Malala's UN speech — an event that garnered headlines around the world.
"First of all please mind that the Taliban never attacked you because of going to school or you were education lover, also please mind that Taliban or Mujahideen are not against the education of any men or women or girl," Rasheed says in the letter.
"Taliban believe that you were intentionally writing against them and running smearing campaign to malign their efforts to establish Islamic system in swat and your writings were provocative."
Rasheed said he was expressing his personal views in the letter, and not those of the Taliban.
The Associated Press said it received the document in an email on Tuesday night. The news agency said it spoke to a second Taliban commander on Wednesday who confirmed its authenticity.